RE: Query on ctakes
Hi, As far as I know, there is no annotations available in cTAKES to extract person specific details as I checked with Sean earlier. May be he can elaborate more on this. Regards, Gandhi -Original Message- From: IBIL Global [mailto:ibilglob...@gmail.com] Sent: Wednesday, May 09, 2018 10:50 AM To: dev@ctakes.apache.org Subject: Query on ctakes Hi Sean, We are currently working on ctakes. while checking the output from ctakes we are not able to get annotations for journal details,author details,reporter details and patient details. Could you please let us know is there any annotations available for above details. Thanks ibil This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender or system manager by email immediately if you have received this e-mail by mistake and delete this e-mail from your system. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited and against the law.
RE: Query on ctakes [EXTERNAL]
Hi Amal, If I am right, the grouping of related information together is not yet available in cTAKES out of the box. Also to generate output in a structured format, you can make use of HTMLWriter. For more detailed info on this, you can check out Sean’s response for “Output formats - CPE - cTAKES - Persist in database<http://mail-archives.apache.org/mod_mbox/ctakes-dev/201803.mbox/ajax/%3CCANs913CB3HVPJOu_EittK%3DMV9H6kD7p6U98xAbWO5QPNV0kd2w%40mail.gmail.com%3E>” thread under http://mail-archives.apache.org/mod_mbox/ctakes-dev/201803.mbox/browser Regards, Gandhi From: ama...@acolade.co.in [mailto:ama...@acolade.co.in] Sent: Monday, March 12, 2018 4:09 PM To: dev@ctakes.apache.org Subject: RE: Query on ctakes [EXTERNAL] Hi Sean, Please find the attachment of input and output text of ctakes. From the ctakes output we can't identify which one is drug, disease, labtest etc. (for example : tocilizumab is a drug, but the output text may not specify what is it?) Also, is there a way where we can group related information together? (e.g:- For each drug, identify the dosage/ root of administration/dosage strength/ Dosage Frequency etc?) How can we generate above expected output in a structured format? (HTML/JSON etc) Thanks & Regards AMAL M 9633746869 - Original Message - Subject: Re: Query on ctakes [EXTERNAL] From: "Finan, Sean" <sean.fi...@childrens.harvard.edu<mailto:sean.fi...@childrens.harvard.edu>> Date: 3/9/18 7:46 pm To: "dev@ctakes.apache.org<mailto:dev@ctakes.apache.org>" <dev@ctakes.apache.org<mailto:dev@ctakes.apache.org>> Hi Amal, Could you please provide a full example sentence with expected vs. produced output? ctakes isn't perfect but something like "fever" should be tagged. Thanks, Sean From: ama...@acolade.co.in<mailto:ama...@acolade.co.in> <ama...@acolade.co.in<mailto:ama...@acolade.co.in>> Sent: Friday, March 9, 2018 12:59 AM To: dev@ctakes.apache.org<mailto:dev@ctakes.apache.org> Subject: Query on ctakes [EXTERNAL] Hello, Am a newbie to cTakes. So far I am able to complete user installation and able to generate the processed output. I am finding the extracted data NOT getting tagged with relevant concepts(contexts) like Drugs, Disease. Lab results etc...which is a real concern. Would appreciate if somebody could help me to achieve tagging of the extracted data. (e:g:- Fever to be tagged as Problem/Disease and abdominopelvic CT as Test(lab test)) Thanks & Regards AMAL M 9633746869 This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender or system manager by email immediately if you have received this e-mail by mistake and delete this e-mail from your system. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited and against the law.
RE: Query on ctakes [EXTERNAL]
Hi Sean, Please find the attachment of input and output text of ctakes. >From the ctakes output we can't identify which one is drug, disease, labtest >etc. (for example : tocilizumab is a drug, but the output text may not specify what is it?) Also, is there a way where we can group related information together? (e.g:- For each drug, identify the dosage/ root of administration/dosage strength/ Dosage Frequency etc?) How can we generate above expected output in a structured format? (HTML/JSON etc) Thanks & Regards AMAL M 9633746869 - Original Message - Subject: Re: Query on ctakes [EXTERNAL] From: "Finan, Sean" <sean.fi...@childrens.harvard.edu> Date: 3/9/18 7:46 pm To: "dev@ctakes.apache.org" <dev@ctakes.apache.org> Hi Amal, Could you please provide a full example sentence with expected vs. produced output? ctakes isn't perfect but something like "fever" should be tagged. Thanks, Sean From: ama...@acolade.co.in <ama...@acolade.co.in> Sent: Friday, March 9, 2018 12:59 AM To: dev@ctakes.apache.org Subject: Query on ctakes [EXTERNAL] Hello, Am a newbie to cTakes. So far I am able to complete user installation and able to generate the processed output. I am finding the extracted data NOT getting tagged with relevant concepts(contexts) like Drugs, Disease. Lab results etc...which is a real concern. Would appreciate if somebody could help me to achieve tagging of the extracted data. (e:g:- Fever to be tagged as Problem/Disease and abdominopelvic CT as Test(lab test)) Thanks & Regards AMAL M 9633746869 cTAKESFast C16091650.0 52 63 tocilizumab polarity:[1], uncertain=[false], subject=[patient], generic=[false], condition=[false], history=[false], doctimerel=[OVERLAP] cTAKESFast C12729190.0 72 76 oralpolarity:[1], uncertain=[false], subject=[patient], generic=[false], condition=[false], history=[false], doctimerel=[OVERLAP] cTAKESFast C02268960.0 72 76 oralpolarity:[1], uncertain=[false], subject=[patient], generic=[false], condition=[false], history=[false] cTAKESFast C38543250.0 77 99 Janus kinase inhibitor polarity:[1], uncertain=[false], subject=[patient], generic=[false], condition=[false], history=[false], doctimerel=[OVERLAP] cTAKESFast C02667000.0 77 82 Janus polarity:[1], uncertain=[false], subject=[patient], generic=[false], condition=[false], history=[false], doctimerel=[OVERLAP] cTAKESFast C00317270.0 83 89 kinase polarity:[1], uncertain=[false], subject=[patient], generic=[false], condition=[false], history=[false], doctimerel=[OVERLAP] cTAKESFast C29306960.0 100 111 tofacitinib polarity:[1], uncertain=[false], subject=[patient], generic=[false], condition=[false], history=[false], doctimerel=[OVERLAP] cTAKESFast C02268750.0 124 152 lower gastrointestinal tractpolarity:[1], uncertain=[false], subject=[patient], generic=[false], condition=[false], history=[false] cTAKESFast C00171890.0 130 152 gastrointestinal tract polarity:[1], uncertain=[false], subject=[patient], generic=[false], condition=[false], history=[false] cTAKESFast C05490990.0 189 200 perforation polarity:[1], uncertain=[false], subject=[patient], generic=[false], condition=[false], history=[false], doctimerel=[OVERLAP] cTAKESFast C00038730.0 263 283 rheumatoid arthritis polarity:[1], uncertain=[false], subject=[patient], generic=[false], condition=[false], history=[false], doctimerel=[OVERLAP] cTAKESFast C00038640.0 274 283 arthritis polarity:[1], uncertain=[false], subject=[patient], generic=[false], condition=[false], history=[false], doctimerel=[OVERLAP] cTAKESFast C00161690.0 317 324 fistula polarity:[1], uncertain=[false], subject=[patient], generic=[false], condition=[false], history=[false], doctimerel=[BEFORE] cTAKESFast C29306960.0 331 342 tofacitinib polarity:[1], uncertain=[false], subject=[patient], generic=[false], condition=[false], history=[false], doctimerel=[BEFORE] cTAKESFast C00871110.0 343 352 treatment polarity:[1], uncertain=[false], subject=[patient], generic=[false], condition=[false], history=[false], doctimerel=[BEFORE] cTAKESFast C37145410.0 409 414 fever polarity:[1], uncertain=[false], subject=[patient], generic=[false], condition=[false], history=[false], doctimerel=[BEFORE] cTAKESFast C00159670.0 409 414 fever polarity:[1], uncertain=[false], subject=[patient], generic=[false], condition=[false], history=[false], doctimere
